Analysis set up

Top loci

MarkerName Chr Pos cytoband gene.context Major Minor MAF Effect StdErr P.value
rs10399947 1 150,861,960 1q21.3 ARNT–[]–SETDB1 G A 0.369 -0.06 0.01 1.02e-08
rs10200279 2 202,170,655 2q33.1 [ALS2CR12] C T 0.287 0.07 0.01 2.67e-09
rs192481803 2 35,336,564 2p22.3 [] C T 0.007 0.65 0.12 2.57e-08
rs62246017 3 71,483,084 3p13 FOXP1—[]—EIF4E3 G A 0.325 0.07 0.01 1.65e-09
rs6791479 3 189,205,032 3q28 TPRG1—[]—TP63 A T 0.427 0.09 0.01 6.09e-15
rs35407 5 33,946,571 5p13.2 [SLC45A2] G A 0.042 -0.47 0.04 3.89e-31
rs4455710 6 32,608,858 6p21.32 [HLA-DQA1] C T 0.368 0.14 0.02 5.57e-21
rs12203592 6 396,321 6p25.3 [IRF4] C T 0.166 0.44 0.01 1.33e-221
rs10944479 6 90,880,393 6q15 [BACH2] G A 0.189 -0.09 0.02 3.75e-09
rs117132860 7 17,134,708 7p21.1 AGR3—[]—AHR G A 0.021 0.25 0.04 7.97e-09
rs7834300 8 116,611,632 8q23.3 [TRPS1] C G 0.438 0.07 0.01 2.01e-09
rs1325118 9 12,619,616 9p23 []–TYRP1 T C 0.304 -0.07 0.01 4.38e-08
rs10810657 9 16,884,586 9p22.2 BNC2–[]—CNTLN A T 0.404 -0.10 0.01 1.26e-17
rs57994353 9 139,356,987 9q34.3 [SEC16A] T C 0.284 0.09 0.01 1.84e-11
rs1126809 11 89,017,961 11q14.3 [TYR] G A 0.279 0.15 0.01 2.21e-38
rs74899442 11 115,890,279 11q23.3 CADM1—[]—BUD13 T C 0.004 0.60 0.11 9.09e-08
rs7939541 11 9,590,389 11p15.4 ZNF143–[]-WEE1 T C 0.410 0.08 0.01 9.23e-12
rs657187 12 52,898,985 12q13.13 KRT6A–[]-KRT5 A G 0.420 -0.07 0.01 1.80e-09
rs721199 12 96,374,057 12q23.1 [HAL] C T 0.463 -0.06 0.01 3.55e-08
rs1800407 15 28,230,318 15q13.1 [OCA2] C T 0.070 0.16 0.02 2.94e-14
rs1805007 16 89,986,117 16q24.3 TCF25-[]-TUBB3 C T 0.078 0.38 0.02 1.36e-87
rs6059655 20 32,665,748 20q11.22 [RALY] G A 0.077 0.25 0.02 1.74e-40

Filter by MAF 1%

Group The number of variats
Total 24,707,509
MAF > 1% 10,792,565
MAF <= 1% 13,914,944

The range of MAF in the original summary stats file was from 0 to 1. Why we have so extremely low MAF? How was MAF computed, using all or a subset of cohorts?

Select a window

Size values: 500Kb, 1Mb, 2Mb around the lead SNP.

Fine-mapping analysis by FINEMAP (3 causals)

Locus1

 - tables of results: `config`, `snp`, `ncausal`
 - locus: 1 
  -- config:
  -- input snps: 2370 fine-mapped + 310 missing Z/LD = 2680 in total
# A tibble: 10 x 4
   rank config                           config_prob config_log10bf
  <int> <chr>                                  <dbl>          <dbl>
1     1 rs10399947,rs12090215,rs78278355       0.167           23.6
2     2 rs1134067,rs12090215,rs78278355        0.130           23.5
3     3 rs6686064,rs12090215,rs78278355        0.113           23.5
# ... with 7 more rows
  -- snp:
# A tibble: 2,680 x 6
  snp        rank_z rank_pp snp_prob snp_prob_cumsum snp_log10bf
  <chr>       <int>   <int>    <dbl>           <dbl>       <dbl>
1 rs12090215     19       1    1.00            0.333       13.2 
2 rs78278355   1446       2    1.00            0.667       13.2 
3 rs10399947      1       3    0.167           0.722        2.50
# ... with 2,677 more rows
  -- 9 snps in 95% credible set: rs12090215, rs78278355, rs10399947, rs1134067, rs6686064, rs11204733, rs4970928, rs6660845, rs11587444...

Locus3

 - tables of results: `config`, `snp`, `ncausal`
 - locus: 1 
  -- config:
  -- input snps: 4148 fine-mapped + 406 missing Z/LD = 4554 in total
# A tibble: 10 x 4
   rank config                config_prob config_log10bf
  <int> <chr>                       <dbl>          <dbl>
1     1 rs72242061                  0.203           3.92
2     2 rs72242061,rs61249550       0.191           7.51
3     3 rs60100018                  0.121           3.69
# ... with 7 more rows
  -- snp:
# A tibble: 4,554 x 6
  snp        rank_z rank_pp snp_prob snp_prob_cumsum snp_log10bf
  <chr>       <int>   <int>    <dbl>           <dbl>       <dbl>
1 rs61249550      3       1    0.475           0.347        3.40
2 rs72242061      1       2    0.395           0.635        3.26
3 rs60100018      2       3    0.184           0.769        2.79
# ... with 4,551 more rows
  -- 4 snps in 95% credible set: rs61249550, rs72242061, rs60100018, rs144368575...

Locus 6

 - tables of results: `config`, `snp`, `ncausal`
 - locus: 1 
  -- config:
  -- input snps: 3278 fine-mapped + 454 missing Z/LD = 3732 in total
# A tibble: 10 x 4
   rank config                         config_prob config_log10bf
  <int> <chr>                                <dbl>          <dbl>
1     1 rs16891982,rs35391,rs1363879     0.998               131.
2     2 rs35407,rs35391,rs1363879        0.00238             128.
3     3 rs16891982,rs35391,rs141759051   0.0000403           126.
# ... with 7 more rows
  -- snp:
# A tibble: 3,732 x 6
  snp        rank_z rank_pp snp_prob snp_prob_cumsum snp_log10bf
  <chr>       <int>   <int>    <dbl>           <dbl>       <dbl>
1 rs35391         9       1    1.00            0.333       13.3 
2 rs1363879      75       2    1.00            0.667        7.73
3 rs16891982      1       3    0.998           0.999        5.96
# ... with 3,729 more rows
  -- 2 snps in 95% credible set: rs35391, rs1363879...

Fine-mapping analysis by FINEMAP (1 causal)

Locus 1

 - tables of results: `config`, `snp`, `ncausal`
 - locus: 1 
  -- config:
  -- input snps: 2370 fine-mapped + 310 missing Z/LD = 2680 in total
# A tibble: 10 x 4
   rank config     config_prob config_log10bf
  <int> <chr>            <dbl>          <dbl>
1     1 rs10399947       0.183           5.54
2     2 rs1134067        0.111           5.32
3     3 rs6686064        0.104           5.29
# ... with 7 more rows
  -- snp:
# A tibble: 2,680 x 6
  snp        rank_z rank_pp snp_prob snp_prob_cumsum snp_log10bf
  <chr>       <int>   <int>    <dbl>           <dbl>       <dbl>
1 rs10399947      1       1    0.183           0.183        2.73
2 rs1134067       2       2    0.111           0.294        2.47
3 rs6686064       3       3    0.104           0.398        2.44
# ... with 2,677 more rows
  -- 9 snps in 95% credible set: rs10399947, rs1134067, rs6686064, rs11587444, rs11204733, rs4970928, rs4970929, rs8444, rs6660845...

Locus 1

 - tables of results: `config`, `snp`, `ncausal`
 - locus: 1 
  -- config:
  -- input snps: 3278 fine-mapped + 454 missing Z/LD = 3732 in total
# A tibble: 10 x 4
   rank config     config_prob config_log10bf
  <int> <chr>            <dbl>          <dbl>
1     1 rs16891982 0.999                 30.5
2     2 rs35407    0.000982              27.5
3     3 rs28777    0.000000913           24.5
# ... with 7 more rows
  -- snp:
# A tibble: 3,732 x 6
  snp        rank_z rank_pp snp_prob snp_prob_cumsum snp_log10bf
  <chr>       <int>   <int>    <dbl>           <dbl>       <dbl>
1 rs16891982      1       1  0.999             0.999       6.52 
2 rs35407         2       2  0.00100           1.00        0.508
3 rs28777         3       3  0.                1.00       -2.52 
# ... with 3,729 more rows
  -- 1 snps in 95% credible set: rs16891982...

Select a window for all 22 loci

Size values: 500Kb, 1Mb, 2Mb around the lead SNP.